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3N9R
Asym. Unit
Info
Asym.Unit (1.2 MB)
Biol.Unit 1 (298 KB)
Biol.Unit 2 (299 KB)
Biol.Unit 3 (299 KB)
Biol.Unit 4 (299 KB)
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(1)
Title
:
CLASS II FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE FROM HELICOBACTER PYLORI IN COMPLEX WITH N-(4-HYDROXYBUTYL)-PHOSPHOGLYCOLOHYDROXAMIC ACID, A COMPETITIVE INHIBITOR
Authors
:
M. Coincon, S. Sygusch
Date
:
31 May 10 (Deposition) - 17 Nov 10 (Release) - 24 Nov 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,K,P,U,Z,e,j
Biol. Unit 1: A,e (1x)
Biol. Unit 2: B,j (1x)
Biol. Unit 3: K,Z (1x)
Biol. Unit 4: P,U (1x)
Keywords
:
Fbp Aldolase, Class Ii, Inhibitor, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Daher, M. Fonvielle, P. M. Gest, M. E. Guerin, M. Jackson, J. Sygusch M. Therisod
Rational Design, Synthesis, And Evaluation Of New Selective Inhibitors Of Microbial Class Ii (Zinc Dependent) Fructose Bis-Phosphate Aldolases.
J. Med. Chem. V. 53 7836 2010
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Hetero Components
(4, 32)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
1e: CHLORIDE ION (CLe)
1f: CHLORIDE ION (CLf)
1g: CHLORIDE ION (CLg)
1h: CHLORIDE ION (CLh)
2a: SODIUM ION (NAa)
2b: SODIUM ION (NAb)
2c: SODIUM ION (NAc)
2d: SODIUM ION (NAd)
2e: SODIUM ION (NAe)
2f: SODIUM ION (NAf)
2g: SODIUM ION (NAg)
2h: SODIUM ION (NAh)
3a: 2-[HYDROXY(4-HYDROXYBUTYL)AMINO]-2... (TD3a)
3b: 2-[HYDROXY(4-HYDROXYBUTYL)AMINO]-2... (TD3b)
3c: 2-[HYDROXY(4-HYDROXYBUTYL)AMINO]-2... (TD3c)
3d: 2-[HYDROXY(4-HYDROXYBUTYL)AMINO]-2... (TD3d)
3e: 2-[HYDROXY(4-HYDROXYBUTYL)AMINO]-2... (TD3e)
3f: 2-[HYDROXY(4-HYDROXYBUTYL)AMINO]-2... (TD3f)
3g: 2-[HYDROXY(4-HYDROXYBUTYL)AMINO]-2... (TD3g)
3h: 2-[HYDROXY(4-HYDROXYBUTYL)AMINO]-2... (TD3h)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
4d: ZINC ION (ZNd)
4e: ZINC ION (ZNe)
4f: ZINC ION (ZNf)
4g: ZINC ION (ZNg)
4h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
8
Ligand/Ion
CHLORIDE ION
2
NA
8
Ligand/Ion
SODIUM ION
3
TD3
8
Ligand/Ion
2-[HYDROXY(4-HYDROXYBUTYL)AMINO]-2-OXOETHYL DIHYDROGENPHOSPHATE
4
ZN
8
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(32, 32)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:83 , HIS A:180 , HIS A:210 , TD3 A:311
BINDING SITE FOR RESIDUE ZN A 308
02
AC2
SOFTWARE
GLN A:47 , HIS A:80 , ASP A:82 , MET A:102 , GLU A:132 , HIS A:210 , LYS A:251 , ASN A:253
BINDING SITE FOR RESIDUE NA A 309
03
AC3
SOFTWARE
ASP A:104 , SER A:106 , GLU A:134 , HOH A:328 , HOH A:657 , HOH A:932 , HOH A:1126
BINDING SITE FOR RESIDUE CL A 310
04
AC4
SOFTWARE
HIS A:83 , HIS A:180 , GLY A:181 , LYS A:184 , HIS A:210 , GLY A:211 , ALA A:212 , SER A:213 , ASN A:253 , ASP A:255 , THR A:256 , ZN A:308 , HOH A:374 , HOH A:807 , HOH A:2493
BINDING SITE FOR RESIDUE TD3 A 311
05
AC5
SOFTWARE
HIS B:83 , HIS B:180 , HIS B:210 , TD3 B:311
BINDING SITE FOR RESIDUE ZN B 308
06
AC6
SOFTWARE
GLN B:47 , HIS B:80 , ASP B:82 , MET B:102 , GLU B:132 , HIS B:210 , LYS B:251 , ASN B:253
BINDING SITE FOR RESIDUE NA B 309
07
AC7
SOFTWARE
ASP B:104 , SER B:106 , GLU B:134 , HOH B:336 , HOH B:814 , HOH B:971 , HOH B:1010
BINDING SITE FOR RESIDUE CL B 310
08
AC8
SOFTWARE
HIS B:83 , HIS B:180 , GLY B:181 , LYS B:184 , HIS B:210 , GLY B:211 , ALA B:212 , SER B:213 , ASN B:253 , ASP B:255 , THR B:256 , ZN B:308 , HOH B:641 , HOH B:779 , HOH B:1770
BINDING SITE FOR RESIDUE TD3 B 311
09
AC9
SOFTWARE
HIS K:83 , HIS K:180 , HIS K:210 , TD3 K:311
BINDING SITE FOR RESIDUE ZN K 308
10
BC1
SOFTWARE
GLN K:47 , HIS K:80 , ASP K:82 , MET K:102 , GLU K:132 , HIS K:210 , LYS K:251 , ASN K:253
BINDING SITE FOR RESIDUE NA K 309
11
BC2
SOFTWARE
ASP K:104 , SER K:106 , GLU K:134 , HOH K:330 , HOH K:589 , HOH K:1424 , HOH K:1565
BINDING SITE FOR RESIDUE CL K 310
12
BC3
SOFTWARE
HIS K:83 , HIS K:180 , GLY K:181 , LYS K:184 , HIS K:210 , GLY K:211 , ALA K:212 , SER K:213 , ASN K:253 , ASP K:255 , THR K:256 , ZN K:308 , HOH K:2453
BINDING SITE FOR RESIDUE TD3 K 311
13
BC4
SOFTWARE
HIS P:83 , HIS P:180 , HIS P:210 , TD3 P:311
BINDING SITE FOR RESIDUE ZN P 308
14
BC5
SOFTWARE
GLN P:47 , HIS P:80 , ASP P:82 , MET P:102 , GLU P:132 , HIS P:210 , LYS P:251 , ASN P:253
BINDING SITE FOR RESIDUE NA P 309
15
BC6
SOFTWARE
ASP P:104 , SER P:106 , GLU P:134 , HOH P:339 , HOH P:397 , HOH P:1789 , HOH P:2376
BINDING SITE FOR RESIDUE CL P 310
16
BC7
SOFTWARE
HOH A:2012 , ASP P:82 , HIS P:83 , HIS P:180 , GLY P:181 , LYS P:184 , HIS P:210 , GLY P:211 , ALA P:212 , SER P:213 , ASN P:253 , ASP P:255 , THR P:256 , ZN P:308 , HOH P:435
BINDING SITE FOR RESIDUE TD3 P 311
17
BC8
SOFTWARE
HIS U:83 , HIS U:180 , HIS U:210 , TD3 U:311
BINDING SITE FOR RESIDUE ZN U 308
18
BC9
SOFTWARE
GLN U:47 , HIS U:80 , ASP U:82 , MET U:102 , GLU U:132 , HIS U:210 , LYS U:251 , ASN U:253
BINDING SITE FOR RESIDUE NA U 309
19
CC1
SOFTWARE
ASP U:104 , SER U:106 , GLU U:134 , HOH U:355 , HOH U:826
BINDING SITE FOR RESIDUE CL U 310
20
CC2
SOFTWARE
ASN U:23 , ASP U:82 , HIS U:83 , HIS U:180 , GLY U:181 , LYS U:184 , HIS U:210 , GLY U:211 , ALA U:212 , SER U:213 , ASN U:253 , ASP U:255 , THR U:256 , ZN U:308
BINDING SITE FOR RESIDUE TD3 U 311
21
CC3
SOFTWARE
HIS Z:83 , HIS Z:180 , HIS Z:210 , TD3 Z:311
BINDING SITE FOR RESIDUE ZN Z 308
22
CC4
SOFTWARE
GLN Z:47 , HIS Z:80 , ASP Z:82 , MET Z:102 , GLU Z:132 , HIS Z:210 , LYS Z:251 , ASN Z:253
BINDING SITE FOR RESIDUE NA Z 309
23
CC5
SOFTWARE
ASP Z:104 , SER Z:106 , GLU Z:134 , HOH Z:324 , HOH Z:1520 , HOH Z:1875
BINDING SITE FOR RESIDUE CL Z 310
24
CC6
SOFTWARE
ASP Z:82 , HIS Z:83 , HIS Z:180 , GLY Z:181 , LYS Z:184 , HIS Z:210 , GLY Z:211 , ALA Z:212 , SER Z:213 , ASN Z:253 , ASP Z:255 , THR Z:256 , ZN Z:308 , HOH Z:1876 , HOH Z:1983
BINDING SITE FOR RESIDUE TD3 Z 311
25
CC7
SOFTWARE
HIS e:83 , HIS e:180 , HIS e:210 , TD3 e:311
BINDING SITE FOR RESIDUE ZN e 308
26
CC8
SOFTWARE
HIS e:80 , ASP e:82 , MET e:102 , GLU e:132 , HIS e:210 , LYS e:251 , ASN e:253
BINDING SITE FOR RESIDUE NA e 309
27
CC9
SOFTWARE
ASP e:104 , SER e:106 , GLU e:134 , HOH e:464
BINDING SITE FOR RESIDUE CL e 310
28
DC1
SOFTWARE
ASN e:23 , ASP e:82 , HIS e:83 , HIS e:180 , GLY e:181 , LYS e:184 , HIS e:210 , GLY e:211 , ALA e:212 , SER e:213 , ASN e:253 , ASP e:255 , THR e:256 , ZN e:308
BINDING SITE FOR RESIDUE TD3 e 311
29
DC2
SOFTWARE
HIS j:83 , HIS j:180 , HIS j:210 , TD3 j:311
BINDING SITE FOR RESIDUE ZN j 308
30
DC3
SOFTWARE
GLN j:47 , HIS j:80 , ASP j:82 , MET j:102 , GLU j:132 , HIS j:210 , LYS j:251 , ASN j:253
BINDING SITE FOR RESIDUE NA j 309
31
DC4
SOFTWARE
ASP j:104 , SER j:106 , GLU j:134 , HOH j:943 , HOH j:1427
BINDING SITE FOR RESIDUE CL j 310
32
DC5
SOFTWARE
ASP j:82 , HIS j:83 , HIS j:180 , GLY j:181 , LYS j:184 , HIS j:210 , GLY j:211 , ALA j:212 , SER j:213 , ASN j:253 , ASP j:255 , THR j:256 , ZN j:308 , HOH j:350 , HOH j:1682
BINDING SITE FOR RESIDUE TD3 j 311
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 8)
Info
All SCOP Domains
1a: SCOP_d3n9ra_ (A:)
1b: SCOP_d3n9rb_ (B:)
1c: SCOP_d3n9re_ (e:)
1d: SCOP_d3n9rj_ (j:)
1e: SCOP_d3n9rk_ (K:)
1f: SCOP_d3n9rp_ (P:)
1g: SCOP_d3n9ru_ (U:)
1h: SCOP_d3n9rz_ (Z:)
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Classes
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(
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Aldolase
(457)
Family
:
automated matches
(113)
Protein domain
:
automated matches
(113)
Helicobacter pylori [TaxId: 290847]
(2)
1a
d3n9ra_
A:
1b
d3n9rb_
B:
1c
d3n9re_
e:
1d
d3n9rj_
j:
1e
d3n9rk_
K:
1f
d3n9rp_
P:
1g
d3n9ru_
U:
1h
d3n9rz_
Z:
[
close SCOP info
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CATH Domains
(0, 0)
Info
all CATH domains
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Label:
Sorry, no Info available
[
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Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_F_bP_aldolase_3n9rZ01 (Z:1-307)
1b: PFAM_F_bP_aldolase_3n9rZ02 (Z:1-307)
1c: PFAM_F_bP_aldolase_3n9rZ03 (Z:1-307)
1d: PFAM_F_bP_aldolase_3n9rZ04 (Z:1-307)
1e: PFAM_F_bP_aldolase_3n9rZ05 (Z:1-307)
1f: PFAM_F_bP_aldolase_3n9rZ06 (Z:1-307)
1g: PFAM_F_bP_aldolase_3n9rZ07 (Z:1-307)
1h: PFAM_F_bP_aldolase_3n9rZ08 (Z:1-307)
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Clans
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)
(
)
Organisms
(
)
(
)
Clan
:
TIM_barrel
(694)
Family
:
F_bP_aldolase
(7)
Helicobacter pylori (strain 51)
(2)
1a
F_bP_aldolase-3n9rZ01
Z:1-307
1b
F_bP_aldolase-3n9rZ02
Z:1-307
1c
F_bP_aldolase-3n9rZ03
Z:1-307
1d
F_bP_aldolase-3n9rZ04
Z:1-307
1e
F_bP_aldolase-3n9rZ05
Z:1-307
1f
F_bP_aldolase-3n9rZ06
Z:1-307
1g
F_bP_aldolase-3n9rZ07
Z:1-307
1h
F_bP_aldolase-3n9rZ08
Z:1-307
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Asym.Unit (1.2 MB)
Header - Asym.Unit
Biol.Unit 1 (298 KB)
Header - Biol.Unit 1
Biol.Unit 2 (299 KB)
Header - Biol.Unit 2
Biol.Unit 3 (299 KB)
Header - Biol.Unit 3
Biol.Unit 4 (299 KB)
Header - Biol.Unit 4
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